The game's Stat Grinding mechanic makes sense for the characters and the context of the story. In every other game, the playable characters are either already experienced in a particular Job, or they can use Crystals to gain immediate knowledge of a Job, so they know how to wield the appropriate weapons and magic. The main characters of Final Fantasy II are just a bunch of orphans who had never fought a battle in their lives, that's why they need to learn how to wield every type of weapon and how to cast every spell all from scratch.
Gordon on first glance looks like a Joke Character, with very low starting HP/MP, bad starting equipment and no magic. However, he actually has surprisingly good stats outside of HP/MP and, given a chance to grow, will easily reach the other three party members in strength. This also really fits his Cowardly Lion character, as he seems himself as a coward and a weakling (represented by his bad starting HP/MP), but when push comes to shove, he's got it (represented by his other stats).
Ultima turning out to be thoroughly mediocre in the NES original is this on a thematic level, even if unintentionally. There's a strong trend in the story of the rebels struggling to eke out victories that turn out to be much smaller than what they hoped for, and Ultima not turning out to be nearly so ultimate as it's fabled to be is a pretty clever microcosm of that.
It's implied, based on the stat increases and the words they say, that the crystals at the top of the Mysidian Tower are in fact the elemental crystals of Final Fantasy II's world. Other games, such as Final Fantasy, Final Fantasy III and Final Fantasy V show that messing with, or even breaking the crystals leads to catastrophic effects on the world. Now, considering that the Empire is willing to unleash the legions of Hell, bomb towns from their Dreadnought and lay waste to them outright with a massive cyclone, what would have happened had the Emperor decided to go after the crystals? Especially given that, unlike in the other games, the crystals are contained in the same room?
As pointed out on the Headscratchers page, the posthumous party led by Minwu makes their way into actual Heaven and finds the "Light Emperor" sitting on the throne. This raises a very disturbing question about who is supposed to be there, and where exactly did they go.
The final stage in Soul of Rebirth is not Heaven, but Arubboth, some kind of Pseudo-Heaven with many hostile monsters or "fallen angels" randomly attacking Minwu and friends. It is very likely that the "Light Emperor" denied access to the real Heaven (assuming it exists in Final Fantasy II universe) even after splitting from the "Dark Emperor", but was unable to return to the world of living and got trapped in limbo realm, which he ended up conquering. It doesn't make it less ominous, though. The "Light Emperor" often sicced his monsters to attack the townsfolk, and if Cid's words are to be believed, those who are trapped in that limbo realm after getting killed by the Emperor and his army can be killed again, and there is no telling what would happen to the victims' souls after they died twice.
Arubboth is implied to be the opposite of Pandemonium, which was the Palace of Hell. Going off of related etymology, it seems like it might've been named after Araboth, which is indeed the Heaven equivalent as far as the seat of power is concerned.
